1
|
Roy S, Roy S, Mahata B, Pramanik J, Hennrich ML, Gavin AC, Teichmann SA. CLICK-chemoproteomics and molecular dynamics simulation reveals pregnenolone targets and their binding conformations in Th2 cells. Front Immunol 2023; 14:1229703. [PMID: 38022565 PMCID: PMC10644475 DOI: 10.3389/fimmu.2023.1229703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 10/05/2023] [Indexed: 12/01/2023] Open
Abstract
Pregnenolone (P5) is synthesized as the first bioactive steroid in the mitochondria from cholesterol. Clusters of differentiation 4 (CD4+) and Clusters of differentiation 8 (CD8+) immune cells synthesize P5 de novo; P5, in turn, play important role in immune homeostasis and regulation. However, P5's biochemical mode of action in immune cells is still emerging. We envisage that revealing the complete spectrum of P5 target proteins in immune cells would have multifold applications, not only in basic understanding of steroids biochemistry in immune cells but also in developing new therapeutic applications. We employed a CLICK-enabled probe to capture P5-binding proteins in live T helper cell type 2 (Th2) cells. Subsequently, using high-throughput quantitative proteomics, we identified the P5 interactome in CD4+ Th2 cells. Our study revealed P5's mode of action in CD4+ immune cells. We identified novel proteins from mitochondrial and endoplasmic reticulum membranes to be the primary mediators of P5's biochemistry in CD4+ and to concur with our earlier finding in CD8+ immune cells. Applying advanced computational algorithms and molecular simulations, we were able to generate near-native maps of P5-protein key molecular interactions. We showed bonds and interactions between key amino acids and P5, which revealed the importance of ionic bond, hydrophobic interactions, and water channels. We point out that our results can lead to designing of novel molecular therapeutics strategies.
Collapse
Affiliation(s)
- Sougata Roy
- Department of Biology, Ashoka University, Rajiv Gandhi Education City, Sonipat, Haryana, India
| | - Sudeep Roy
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
| | - Bidesh Mahata
- Division of Immunology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Jhuma Pramanik
- Division of Immunology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Marco L. Hennrich
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, EMBL, Heidelberg, Germany
- Cellzome, a GlaxoSmithKline (GSK) company, Genomic Sciences, Pharma R&D, Heidelberg, Germany
| | - Anne-Claude Gavin
- Department for Cell Physiology and Metabolism, Centre Medical Universitaire, University of Geneva, Geneva, Switzerland
- Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Sarah A. Teichmann
- Cellular Genetics, Wellcome Sanger Institute, Cambridge, United Kingdom
- Theory of Condensed Matter, Cavendish Laboratory, Cambridge, United Kingdom
| |
Collapse
|
2
|
Chakraborty S, Pramanik J, Mahata B. Revisiting steroidogenesis and its role in immune regulation with the advanced tools and technologies. Genes Immun 2021; 22:125-140. [PMID: 34127827 PMCID: PMC8277576 DOI: 10.1038/s41435-021-00139-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 05/03/2021] [Accepted: 05/21/2021] [Indexed: 12/19/2022]
Abstract
Historically tools and technologies facilitated scientific discoveries. Steroid hormone research is not an exception. Unfortunately, the dramatic advancement of the field faded this research area and flagged it as a solved topic. However, it should have been the opposite. The area should glitter with its strong foundation and attract next-generation scientists. Over the past century, a myriad of new facts on biochemistry, molecular biology, cell biology, physiology and pathology of the steroid hormones was discovered. Several innovations were made and translated into life-saving treatment strategies such as synthetic steroids, and inhibitors of steroidogenesis and steroid signaling. Steroid molecules exhibit their diverse effects on cell metabolism, salt and water balance, development and function of the reproductive system, pregnancy, and immune-cell function. Despite vigorous research, the molecular basis of the immunomodulatory effect of steroids is still mysterious. The recent excitement on local extra-glandular steroidogenesis in regulating inflammation and immunity is revitalizing the topic with a new perspective. Therefore, here we review the role of steroidogenesis in regulating inflammation and immunity, discuss the unresolved questions, and how this area can bring another golden age of steroid hormone research with the development of new tools and technologies and advancement of the scientific methods.
Collapse
Affiliation(s)
| | - Jhuma Pramanik
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Bidesh Mahata
- Department of Pathology, University of Cambridge, Cambridge, UK.
| |
Collapse
|
3
|
Haim-Vilmovsky L, Henriksson J, Walker JA, Miao Z, Natan E, Kar G, Clare S, Barlow JL, Charidemou E, Mamanova L, Chen X, Proserpio V, Pramanik J, Woodhouse S, Protasio AV, Efremova M, Griffin JL, Berriman M, Dougan G, Fisher J, Marioni JC, McKenzie ANJ, Teichmann SA. Mapping Rora expression in resting and activated CD4+ T cells. PLoS One 2021; 16:e0251233. [PMID: 34003838 PMCID: PMC8130942 DOI: 10.1371/journal.pone.0251233] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 04/22/2021] [Indexed: 11/19/2022] Open
Abstract
The transcription factor Rora has been shown to be important for the development of ILC2 and the regulation of ILC3, macrophages and Treg cells. Here we investigate the role of Rora across CD4+ T cells in general, but with an emphasis on Th2 cells, both in vitro as well as in the context of several in vivo type 2 infection models. We dissect the function of Rora using overexpression and a CD4-conditional Rora-knockout mouse, as well as a RORA-reporter mouse. We establish the importance of Rora in CD4+ T cells for controlling lung inflammation induced by Nippostrongylus brasiliensis infection, and have measured the effect on downstream genes using RNA-seq. Using a systematic stimulation screen of CD4+ T cells, coupled with RNA-seq, we identify upstream regulators of Rora, most importantly IL-33 and CCL7. Our data suggest that Rora is a negative regulator of the immune system, possibly through several downstream pathways, and is under control of the local microenvironment.
Collapse
MESH Headings
- Animals
- Antigens, Helminth/immunology
- Antigens, Helminth/metabolism
- CD4-Positive T-Lymphocytes/immunology
- Cells, Cultured
- Cytokines/metabolism
- Disease Models, Animal
- Female
- Gene Expression Regulation/immunology
- Lymphocyte Activation
- Macrophages/immunology
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Mice, Transgenic
- Nippostrongylus/immunology
- Nuclear Receptor Subfamily 1, Group F, Member 1/immunology
- Nuclear Receptor Subfamily 1, Group F, Member 1/metabolism
- Pneumonia/immunology
- Pneumonia/parasitology
- Pneumonia/pathology
- Strongylida Infections/immunology
- Strongylida Infections/parasitology
- Th2 Cells/immunology
Collapse
Affiliation(s)
- Liora Haim-Vilmovsky
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Johan Henriksson
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Jennifer A. Walker
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Zhichao Miao
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Eviatar Natan
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Gozde Kar
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Simon Clare
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Jillian L. Barlow
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Evelina Charidemou
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Xi Chen
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Valentina Proserpio
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Jhuma Pramanik
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Steven Woodhouse
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust—Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Anna V. Protasio
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Mirjana Efremova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Julian L. Griffin
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Metabolism, Digestion and Reproduction, Biomolecular Medicine, Imperial College London, London, United Kingdom
| | - Matt Berriman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Gordon Dougan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | | | - John C. Marioni
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Andrew N. J. McKenzie
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Sarah A. Teichmann
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Theory of Condensed Matter, Cavendish Laboratory, Cambridge, United Kingdom
| |
Collapse
|
4
|
Roy S, Sipthorp J, Mahata B, Pramanik J, Hennrich ML, Gavin AC, Ley SV, Teichmann SA. CLICK-enabled analogues reveal pregnenolone interactomes in cancer and immune cells. iScience 2021; 24:102485. [PMID: 34036248 PMCID: PMC8138728 DOI: 10.1016/j.isci.2021.102485] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 01/27/2021] [Accepted: 04/26/2021] [Indexed: 11/27/2022] Open
Abstract
Pregnenolone (P5) promotes prostate cancer cell growth, and de novo synthesis of intratumoural P5 is a potential cause of development of castration resistance. Immune cells can also synthesize P5 de novo. Despite its biological importance, little is known about P5's mode of actions, which appears to be context dependent and pleiotropic. A comprehensive proteome-wide spectrum of P5-binding proteins that are involved in its trafficking and functionality remains unknown. Here, we describe an approach that integrates chemical biology for probe synthesis with chemoproteomics to map P5-protein interactions in live prostate cancer cells and murine CD8+ T cells. We subsequently identified P5-binding proteins potentially involved in P5-trafficking and in P5's non-genomic action that may drive the promotion of castrate-resistance prostate cancer and regulate CD8+ T cell function. We envisage that this methodology could be employed for other steroids to map their interactomes directly in a broad range of living cells, tissues, and organisms. Developed four functional click-enabled analogues of pregnenolone (P5) Chemoproteomics prioritizes 62 P5 target proteins in live cancer and immune cells These include shared and distinct biochemical role of P5 in cancer and immune cells P5 activity in cancer and immune cells is mediated through non-genomic pathways
Collapse
Affiliation(s)
- Sougata Roy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.,Ashoka University, Rajiv Gandhi Education City, Sonipat, Haryana 131029, India
| | - James Sipthorp
- The Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Bidesh Mahata
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.,Division of Immunology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Jhuma Pramanik
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,Division of Immunology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Marco L Hennrich
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, EMBL, Heidelberg, Germany
| | - Anne-Claude Gavin
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, EMBL, Heidelberg, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, EMBL, Heidelberg, Germany.,University of Geneva, Department for Cell Physiology and Metabolism, Centre Medical Universitaire, Rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland
| | - Steven V Ley
- The Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,Theory of Condensed Matter, Cavendish Laboratory, 19 JJ Thomson Avenue, Cambridge CB3 0HE, UK
| |
Collapse
|
5
|
Mahata B, Pramanik J, van der Weyden L, Polanski K, Kar G, Riedel A, Chen X, Fonseca NA, Kundu K, Campos LS, Ryder E, Duddy G, Walczak I, Okkenhaug K, Adams DJ, Shields JD, Teichmann SA. Tumors induce de novo steroid biosynthesis in T cells to evade immunity. Nat Commun 2020; 11:3588. [PMID: 32680985 PMCID: PMC7368057 DOI: 10.1038/s41467-020-17339-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 06/22/2020] [Indexed: 12/23/2022] Open
Abstract
Tumors subvert immune cell function to evade immune responses, yet the complex mechanisms driving immune evasion remain poorly understood. Here we show that tumors induce de novo steroidogenesis in T lymphocytes to evade anti-tumor immunity. Using a transgenic steroidogenesis-reporter mouse line we identify and characterize de novo steroidogenic immune cells, defining the global gene expression identity of these steroid-producing immune cells and gene regulatory networks by using single-cell transcriptomics. Genetic ablation of T cell steroidogenesis restricts primary tumor growth and metastatic dissemination in mouse models. Steroidogenic T cells dysregulate anti-tumor immunity, and inhibition of the steroidogenesis pathway is sufficient to restore anti-tumor immunity. This study demonstrates T cell de novo steroidogenesis as a mechanism of anti-tumor immunosuppression and a potential druggable target.
Collapse
Affiliation(s)
- Bidesh Mahata
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| | - Jhuma Pramanik
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | | | - Krzysztof Polanski
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Gozde Kar
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- Translational Medicine, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Angela Riedel
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, Cambridge, UK
| | - Xi Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Nuno A Fonseca
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Kousik Kundu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
| | - Lia S Campos
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Edward Ryder
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Graham Duddy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Izabela Walczak
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Klaus Okkenhaug
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - David J Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jacqueline D Shields
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, Cambridge, UK.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
- Theory of Condensed Matter, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge, CB3 0HE, UK.
| |
Collapse
|
6
|
Davidson S, Efremova M, Riedel A, Mahata B, Pramanik J, Huuhtanen J, Kar G, Vento-Tormo R, Hagai T, Chen X, Haniffa MA, Shields JD, Teichmann SA. Single-Cell RNA Sequencing Reveals a Dynamic Stromal Niche That Supports Tumor Growth. Cell Rep 2020; 31:107628. [PMID: 32433953 PMCID: PMC7242909 DOI: 10.1016/j.celrep.2020.107628] [Citation(s) in RCA: 156] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 01/22/2020] [Accepted: 04/18/2020] [Indexed: 12/20/2022] Open
Abstract
Here, using single-cell RNA sequencing, we examine the stromal compartment in murine melanoma and draining lymph nodes (LNs) at points across tumor development, providing data at http://www.teichlab.org/data/. Naive lymphocytes from LNs undergo activation and clonal expansion within the tumor, before PD1 and Lag3 expression, while tumor-associated myeloid cells promote the formation of a suppressive niche. We identify three temporally distinct stromal populations displaying unique functional signatures, conserved across mouse and human tumors. Whereas "immune" stromal cells are observed in early tumors, "contractile" cells become more prevalent at later time points. Complement component C3 is specifically expressed in the immune population. Its cleavage product C3a supports the recruitment of C3aR+ macrophages, and perturbation of C3a and C3aR disrupts immune infiltration, slowing tumor growth. Our results highlight the power of scRNA-seq to identify complex interplays and increase stromal diversity as a tumor develops, revealing that stromal cells acquire the capacity to modulate immune landscapes from early disease.
Collapse
Affiliation(s)
- Sarah Davidson
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/Medical Research Council Research Centre, Box 197 Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Mirjana Efremova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Angela Riedel
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/Medical Research Council Research Centre, Box 197 Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Bidesh Mahata
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Department of Pathology, University of Cambridge, Cambridge, UK
| | - Jhuma Pramanik
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Jani Huuhtanen
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Gozde Kar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Tzachi Hagai
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Xi Chen
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Muzlifah A Haniffa
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Jacqueline D Shields
- Medical Research Council Cancer Unit, University of Cambridge, Hutchison/Medical Research Council Research Centre, Box 197 Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Cavendish Laboratory, University of Cambridge, JJ Thomson Ave, Cambridge CB3 0HE, UK.
| |
Collapse
|
7
|
Henriksson J, Chen X, Gomes T, Ullah U, Meyer KB, Miragaia R, Duddy G, Pramanik J, Yusa K, Lahesmaa R, Teichmann SA. Genome-wide CRISPR Screens in T Helper Cells Reveal Pervasive Crosstalk between Activation and Differentiation. Cell 2019; 176:882-896.e18. [PMID: 30639098 PMCID: PMC6370901 DOI: 10.1016/j.cell.2018.11.044] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 09/19/2018] [Accepted: 11/28/2018] [Indexed: 12/24/2022]
Abstract
T helper type 2 (Th2) cells are important regulators of mammalian adaptive immunity and have relevance for infection, autoimmunity, and tumor immunology. Using a newly developed, genome-wide retroviral CRISPR knockout (KO) library, combined with RNA-seq, ATAC-seq, and ChIP-seq, we have dissected the regulatory circuitry governing activation and differentiation of these cells. Our experiments distinguish cell activation versus differentiation in a quantitative framework. We demonstrate that these two processes are tightly coupled and are jointly controlled by many transcription factors, metabolic genes, and cytokine/receptor pairs. There are only a small number of genes regulating differentiation without any role in activation. By combining biochemical and genetic data, we provide an atlas for Th2 differentiation, validating known regulators and identifying factors, such as Pparg and Bhlhe40, as part of the core regulatory network governing Th2 helper cell fates.
Collapse
Affiliation(s)
- Johan Henriksson
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK; Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7, Novum, SE-141 83, Huddinge, Sweden
| | - Xi Chen
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Tomás Gomes
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ubaid Ullah
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6 FI-20520, Turku, Finland
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ricardo Miragaia
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Graham Duddy
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jhuma Pramanik
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Kosuke Yusa
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6 FI-20520, Turku, Finland
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK; EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK; Theory of Condensed Matter, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge CB3 0HE, UK.
| |
Collapse
|
8
|
Pramanik J, Chen X, Kar G, Henriksson J, Gomes T, Park JE, Natarajan K, Meyer KB, Miao Z, McKenzie ANJ, Mahata B, Teichmann SA. Genome-wide analyses reveal the IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation. Genome Med 2018; 10:76. [PMID: 30355343 PMCID: PMC6199730 DOI: 10.1186/s13073-018-0589-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 10/12/2018] [Indexed: 12/24/2022] Open
Abstract
Background The IRE1a-XBP1 pathway is a conserved adaptive mediator of the unfolded protein response. The pathway is indispensable for the development of secretory cells by facilitating protein folding and enhancing secretory capacity. In the immune system, it is known to function in dendritic cells, plasma cells, and eosinophil development and differentiation, while its role in T helper cell is unexplored. Here, we investigated the role of the IRE1a-XBP1 pathway in regulating activation and differentiation of type-2 T helper cell (Th2), a major T helper cell type involved in allergy, asthma, helminth infection, pregnancy, and tumor immunosuppression. Methods We perturbed the IRE1a-XBP1 pathway and interrogated its role in Th2 cell differentiation. We performed genome-wide transcriptomic analysis of differential gene expression to reveal IRE1a-XBP1 pathway-regulated genes and predict their biological role. To identify direct target genes of XBP1 and define XBP1’s regulatory network, we performed XBP1 ChIPmentation (ChIP-seq). We validated our predictions by flow cytometry, ELISA, and qPCR. We also used a fluorescent ubiquitin cell cycle indicator mouse to demonstrate the role of XBP1 in the cell cycle. Results We show that Th2 lymphocytes induce the IRE1a-XBP1 pathway during in vitro and in vivo activation. Genome-wide transcriptomic analysis of differential gene expression by perturbing the IRE1a-XBP1 pathway reveals XBP1-controlled genes and biological pathways. Performing XBP1 ChIPmentation (ChIP-seq) and integrating with transcriptomic data, we identify XBP1-controlled direct target genes and its transcriptional regulatory network. We observed that the IRE1a-XBP1 pathway controls cytokine secretion and the expression of two Th2 signature cytokines, IL13 and IL5. We also discovered that the IRE1a-XBP1 pathway facilitates activation-dependent Th2 cell proliferation by facilitating cell cycle progression through S and G2/M phase. Conclusions We confirm and detail the critical role of the IRE1a-XBP1 pathway during Th2 lymphocyte activation in regulating cytokine expression, secretion, and cell proliferation. Our high-quality genome-wide XBP1 ChIP and gene expression data provide a rich resource for investigating XBP1-regulated genes. We provide a browsable online database available at http://data.teichlab.org. Electronic supplementary material The online version of this article (10.1186/s13073-018-0589-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jhuma Pramanik
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Xi Chen
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Gozde Kar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Johan Henriksson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Tomás Gomes
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jong-Eun Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Kedar Natarajan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Zhichao Miao
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Andrew N J McKenzie
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Bidesh Mahata
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. .,EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. .,EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. .,Theory of Condensed Matter, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge, CB3 0HE, UK.
| |
Collapse
|
9
|
Proserpio V, Piccolo A, Haim-Vilmovsky L, Kar G, Lönnberg T, Svensson V, Pramanik J, Natarajan KN, Zhai W, Zhang X, Donati G, Kayikci M, Kotar J, McKenzie ANJ, Montandon R, James KR, Fernandez-Ruiz D, Heath WR, Haque A, Billker O, Woodhouse S, Cicuta P, Nicodemi M, Teichmann SA. Erratum to: Single cell analysis of CD4+ T cell differentiation reveals three major cell states and progressive acceleration of proliferation. Genome Biol 2016; 17:133. [PMID: 27333907 PMCID: PMC4918121 DOI: 10.1186/s13059-016-0998-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 06/06/2016] [Indexed: 11/18/2022] Open
Affiliation(s)
- Valentina Proserpio
- EMBL, European Bioinformatics Institute (EBI), Hinxton, CB10 1SD, UK.,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Andrea Piccolo
- Department of Physics, CNR-Spin, Istituto Nazionale di Fisica Nucleare (INFN), University of Naples Federico II, Napoli, Italy
| | - Liora Haim-Vilmovsky
- EMBL, European Bioinformatics Institute (EBI), Hinxton, CB10 1SD, UK.,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Gozde Kar
- EMBL, European Bioinformatics Institute (EBI), Hinxton, CB10 1SD, UK
| | - Tapio Lönnberg
- EMBL, European Bioinformatics Institute (EBI), Hinxton, CB10 1SD, UK.,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | | | - Jhuma Pramanik
- EMBL, European Bioinformatics Institute (EBI), Hinxton, CB10 1SD, UK.,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Kedar Nath Natarajan
- EMBL, European Bioinformatics Institute (EBI), Hinxton, CB10 1SD, UK.,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Weichao Zhai
- Cavendish Laboratory, University of Cambridge, Madingley Road, Cambridge, CB3 0HE, United Kingdom
| | - Xiuwei Zhang
- EMBL, European Bioinformatics Institute (EBI), Hinxton, CB10 1SD, UK
| | - Giacomo Donati
- Centre for Stem Cells and Regenerative Medicine, Kings College London, London, SE1 9RT, UK
| | - Melis Kayikci
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Jurij Kotar
- Cavendish Laboratory, University of Cambridge, Madingley Road, Cambridge, CB3 0HE, United Kingdom
| | | | - Ruddy Montandon
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Kylie R James
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Daniel Fernandez-Ruiz
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - William R Heath
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.,The Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Melbourne, Parkville, Australia
| | - Ashraful Haque
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Oliver Billker
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Steven Woodhouse
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Pietro Cicuta
- Cavendish Laboratory, University of Cambridge, Madingley Road, Cambridge, CB3 0HE, United Kingdom
| | - Mario Nicodemi
- Department of Physics, CNR-Spin, Istituto Nazionale di Fisica Nucleare (INFN), University of Naples Federico II, Napoli, Italy.
| | - Sarah A Teichmann
- EMBL, European Bioinformatics Institute (EBI), Hinxton, CB10 1SD, UK. .,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| |
Collapse
|
10
|
Ray S, Pramanik J, Bhattacharyya M, Todi S. Prospective observational evaluation of incidences and implications of drug-drug interactions induced adverse drug reactions in critically ill patients. Indian J Pharm Sci 2011; 72:787-92. [PMID: 21969755 PMCID: PMC3178984 DOI: 10.4103/0250-474x.84597] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 08/13/2010] [Accepted: 11/08/2010] [Indexed: 12/04/2022] Open
Abstract
The primary aim of this study is to identify and analyze the importance of adverse drug reaction due to drug-drug interaction as a contributing factor towards drug safety. Patients more than 18 years of age admitted in multidisciplinary intensive care unit of a tertiary care hospital were included in this study. Patients who stayed less than 48 h and patients in whom all treatment modalities have been withdrawn and were on comfort measures only (no drugs were prescribed), were excluded. All the drugs that were given during intensive care unit stay were checked for presence of potential interactions which led to adverse drug reaction. Drug-drug interactions that were detected clinically or through investigations were recorded and also any therapeutic actions taken for drug-drug interactions were noted. From June 2006 to April 2007, 400 patients-prescriptions were analyzed. Adverse drug reactions due to drug-drug interactions were identified in 64% patients. Among those patients 38.67% had a single drug-drug interaction. Potential drug-drug interactions were 602. Clinically significant drug-drug interactions among the potential were 208 (34.55%). Clinically relevant drug-drug interactions were 103 (49.52% of 208 episodes). The adverse drug reactions due to drug-drug interactions in our sample were managed either by substituting another drug (50.48% of 103 episodes) or by adjusting the dose (1% of 103 episodes) or by omitting the drug (48.54% of 103 episodes). Among the 208 observed drug-drug interactions induced adverse drug reactions 21.63% was severe drug-drug interactions induced adverse drug reactions, 23.08% was moderate drug-drug interactions induced adverse drug reactions and 55.29% was minor drug-drug interactions induced adverse drug reactions. The interactions which were life threatening and/ or require medical intervention to minimize or prevent serious adverse effects were considered as severe drug-drug interactions and those interaction which resulted in an exacerbation of the patient's condition and/ or require an alteration in therapy were considered as moderate drug-drug interactions. The interactions which were limited clinical effects and manifestations may include an increase in the frequency or severity of side effects but generally would not require a major alteration in therapy were classified as minor drug-drug interactions. The correlation coefficient was 0.86 between the number of drugs given to the patient & number of average potential adverse drug reactions found among the patients. Increase in number of prescribed drug significantly (one way) increases number of potential adverse drug reaction due to drug-drug interaction (p<0.0001). Critically ill patients are more susceptible to drug-drug interactions due to the administration of multiple drugs and complex drug combinations. Several drug-drug interactions were clinically irrelevant.
Collapse
Affiliation(s)
- S Ray
- Department of Pharmaceutical Technology, Jadavpur University, Raja S. C. Mallick Road, Kolkata-700 032, India
| | | | | | | |
Collapse
|
11
|
|
12
|
Pramanik J, Prasad G, Sen A, Kaw PK. Experimental observations of transverse shear waves in strongly coupled dusty plasmas. Phys Rev Lett 2002; 88:175001. [PMID: 12005765 DOI: 10.1103/physrevlett.88.175001] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2001] [Indexed: 05/23/2023]
Abstract
We report experimental observations of transverse shear waves in a three-dimensional dusty plasma that is in the strongly coupled fluid regime. These spontaneous oscillations occur when the ambient neutral pressure is reduced below a threshold value and the measured dispersion characteristics of these waves are found to be in good agreement with predictions of a viscoelastic theory of dusty plasmas.
Collapse
Affiliation(s)
- J Pramanik
- Institute for Plasma Research, Bhat, Gandhinagar 382428, India
| | | | | | | |
Collapse
|
13
|
Pramanik J, Lodam AN, Badole CM, Reddy MV, Patond KR, Harinath BC. Detection of tubercular antibody and antigen in sera of bone and joint tuberculosis. Indian J Clin Biochem 2000; 15:22-8. [PMID: 23105233 DOI: 10.1007/bf02873543] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Trichloroacetic acid (TCA) solubilized and DEAE fractionatedMycobacterium tuberculosis H(37)Ra excretory-secretory (ES) antigen viz., Mtb EST DE1 and affinity purified goat antibodies to the TCA solubilized ES antigen (Mtb EST) were explored in detecting tubercular antibody and antigen respectively in sera of bone and joint tuberculosis by indirect and sandwich ELISA. Out of total 36 bone & joint tuberculosis cases, tubercular antibody was detected by indirect ELISA in 30 patients (sensitivity 83%), while circulating tubercular antigen was detected by sandwich ELISA in 27 patients (sensitivity 75%). Out of 34 non tubercular disease control cases, 10 patients showed positive reaction for antibody while only 4 patients showed positive reaction for antigen. In another group of 34 healthy subjects who were screened, 4 individuals showed positive reaction for tubercular antibody and 2 cases for antigen. This study shows that antigen detection assay using affinity purified anti Mtb EST antigen antibody is superior with overall specificity of 91% as compared to antibody detection assay with 75% specificity in bone & joint tuberculosis.
Collapse
Affiliation(s)
- J Pramanik
- Jamnalal Bajaj Tropical Disease Research Centre & Department of Biochemistry, Mahatma Gandhi Institute of Medical Sciences, 442 102 Sevagram (Wardha)
| | | | | | | | | | | |
Collapse
|
14
|
Abstract
The amino acid composition of proteins and the fatty acid composition of the cell membranes were measured in Escherichia coli growing exponentially in batch culture on glucose, succinate, glycerol, pyruvate, and acetate, and growing under continuous culture conditions on glucose at dilutions rates equivalent to the growth rates of the batch cultures. Although the fatty acid composition of the membranes did change significantly with carbon source and dilution rate, the amino acid content of proteins did not change significantly under either condition. A previously developed stoichiometric model of metabolism was used to calculate the fluxes through the metabolic reactions and to determine their sensitivity to changes in fatty acid and amino acid composition.
Collapse
Affiliation(s)
- J Pramanik
- Department of Chemical Engineering, University of California, Berkeley, California 94720-1462, USA
| | | |
Collapse
|
15
|
Abstract
Polyphosphate metabolism plays an important role in the bioremediation of phosphate contamination in municipal wastewater, and may play a key role in heavy metal tolerance and bioremediation. However, little is known about the regulation of polyphosphate metabolism in microorganisms and its role in heavy metal toxicity. We have manipulated polyphosphate metabolism in Escherichia coli by overexpressing the genes for polyphosphate kinase (ppk) and for polyphosphatase (ppx) under control of their native promoters and inducible promoters. Overexpression of ppk results in high levels of intracellular polyphosphate, improved phosphate uptake, but no increase in tolerance to heavy metals. Overexpression of both ppk and ppx results in lower levels of intracellular polyphosphate, secretion of phosphate from the cell, and increased tolerance to heavy metals. Metabolic flux analysis indicates that the cell responds to increased flux through the PPK-PPX pathway by altering flux through the TCA cycle.
Collapse
Affiliation(s)
- J D Keasling
- Department of Chemical Engineering, University of California, Berkeley, California 94720-1462, USA.
| | | | | |
Collapse
|
16
|
Pramanik J, Keasling JD. Stoichiometric model ofEscherichia coli metabolism: Incorporation of growth-rate dependent biomass composition and mechanistic energy requirements. Biotechnol Bioeng 1997; 56:398-421. [DOI: 10.1002/(sici)1097-0290(19971120)56:4<398::aid-bit6>3.0.co;2-j] [Citation(s) in RCA: 255] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|